Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_011766578.1 AZO_RS14335 aldehyde dehydrogenase family protein
Query= BRENDA::Q97YT9 (492 letters) >NCBI__GCF_000061505.1:WP_011766578.1 Length = 477 Score = 215 bits (547), Expect = 3e-60 Identities = 147/480 (30%), Positives = 232/480 (48%), Gaps = 23/480 (4%) Query: 16 KLYINGEFIDSKTDTIGKAYNPAKDEIIAEVPFSAKDEVEEAIQSAQEAFEKWREVPITT 75 +L+I G ++ +P+ D + A +P A + E A+ +A AF+ W P+ Sbjct: 7 QLFIGGRWVAPVRTGFIDVMDPSTDTVFARIPEGAAADAEAAVAAAHAAFDAWSRTPLAE 66 Query: 76 RIQYLFALKNRLEEYSETIARIIVQNHGKTIQEARGDMRRTIENVEAAISAAYTLYKGEH 135 R + + L+ S+ +A +I G + + A + L+ + Sbjct: 67 RAGCIERIAAGLKARSDELAHVIACEVGMP------------KKLAARVQVGGPLWHWNN 114 Query: 136 LDQVSQEVD-------ETVVREPLGVFGIITPFNFPTMVPFWFLPYAIVLGNTVVVKPSE 188 + +++ + VVREP+GV G ITP+NFP + A++ G TVV+KPSE Sbjct: 115 YEALARSFEWERRVGNSLVVREPIGVVGAITPWNFPLNQITLKVAPALLAGCTVVLKPSE 174 Query: 189 ITPVPMDFIIRIFDEIKLPRGVVNVVHGAKDVVDEFL-TNKLVQGVTFVGSTRVGKYIYE 247 + P+ + I + +P GV N+V G VV E L ++ V V+F GSTR G+ + E Sbjct: 175 VAPINAFILAEIIEAAGVPAGVFNLVTGYGPVVGEVLASDPRVDMVSFTGSTRAGRRVAE 234 Query: 248 NAGKNGKKAIVQAGAKNFVVVMPDADLNKAIPSIVSAFFGNAGQRCLAAANLVAVGNIYD 307 A KK ++ G K+ VV+ DADL A+ VS+ N+GQ C A L+ D Sbjct: 235 LAAATVKKVALELGGKSASVVLDDADLAAAVKGTVSSCLLNSGQTCSAHTRLLVPRARLD 294 Query: 308 EVKRKFIEASKQLKIGYGLDESVDMGPVVTKDAKKRIIGYIEKGIEEGAKLLLDGRDVKV 367 E + A+ +K G L E +GP+V+ ++R+ YI +G+ EGA+L G + Sbjct: 295 EAAQLAATAASAMKPGPALAEDSRLGPLVSAAQRERVRDYIRRGVAEGARLACGGAEPPA 354 Query: 368 PEYPNGYFLGPTVFDEVTPEMVIAKEEIFGPVASIIHVKNLDEAINIINRSNYGNASSIF 427 E GYF+ PTV +A+EEIFGPV ++ ++AI I N S YG A +++ Sbjct: 355 -ELEQGYFVQPTVLVCEDSRATVAQEEIFGPVLVVLPHDGDEDAIRIANDSPYGLAGAVW 413 Query: 428 TTSGYYARKFRREVNTGNIGINIGVAAPMAFFPFGGRKESFFGILHGQIDSVDFFTDKKV 487 + A R + TG + IN P A PFGG K+S G +G+ +F K + Sbjct: 414 AGNEERALAVARRLRTGQVDINGAAWNPRA--PFGGYKQSGLGRENGEYGLDEFLQYKAI 471 Lambda K H 0.319 0.139 0.398 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 497 Number of extensions: 18 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 492 Length of database: 477 Length adjustment: 34 Effective length of query: 458 Effective length of database: 443 Effective search space: 202894 Effective search space used: 202894 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory